This blue musical instrument plays a distinct melody that can summon a Duck that transports the user to certain areas of Hyrule. The Flute was once owned by a boy from Kakariko Village who was warped to the Dark World and transformed into a tapir. Link discovers him in the Dark World, and he tells him to find his Flute, which was buried near the stump in the Haunted Grove in the Light World. To aid him in this endeavor, he gives Link a Shovel.

Link unearths the Flute from a patch of flowers in the northwest corner of the Haunted Grove and brings it back to the Dark World, where he plays it for the boy, who finds he cannot play it himself, and is soothed by the music and subsequently transforms further into an inanimate tree. Link can then play the melody of the Flute for the Weathercock in Kakariko Village. The statue shatters, revealing the flying bird inside. The bird transports Link to certain areas of the Light World when the Flute is played again, as long as Link is in the overworld of the Light World. All of these warp points are located near an entrance to the Dark World.

Near the end of his quest, Link uses the Flute to call the bird, who takes him to the Pyramid to take on Ganon. This is the only time that the Flute has any effect in the Dark World.

Despite its name, the Flute appears to be an Ocarina, and is called such in the original Japanese version of the game. The design of the flute is very similar to the iconic Ocarina of Time from later games in the series, and may well have served as the inspiration for said item.